Heaven's Mistake
by iamthesquidoflegend
Summary: The plan was to stab Sebastian with the sword containing Jace's Heavenly Fire, which would kill him and end the madness. However, he miraculously survived. The war is supposedly over, but how can they tell for sure with Jonathan living among them? WARNING: Spoilers from City of Heavenly Fire
1. The Mistake

Clary drove the sword into Sebastian's chest, feeling his bones snap, feeling the blade push through skin and muscle. She was horrified at what she was doing and for a dizzying moment her vision clouded.

His eyes widened and she could see them so clearly, black holes trying to drown her in their emptiness.

"Clary," he gasped, his voice raspy. He gripped the hilt of Heosphoros and wrenched it from his body, splattering her with blackish blood.

His knees buckled, sending him pitching backward. The sword clattered to the ground, spinning out of reach. His limbs jerked and twitched.

Clary watched with a kind of horrified fascination, disgusted but unable to avert her eyes.

He had bragged about being invincible, but here he was, dying before her, a gaping hole in his chest.

Clary fell to her knees, tears of shock and horror sliding down her face, splashing down on her hands. She ignored them as she sat beside her brother, gazing into his eyes.

There was a spark of light in his wound, brightening until it was a flame, licking at his clothes, spreading until it coated him in its fiery embrace. She could feel the heat of the heavenly fire washing over her, but she didn't move. She stared, transfixed, as Sebastian lit up like a beacon.

Jocelyn ran over and knelt next to her daughter. Clary didn't bother looking over to see the expression on her mother's face.

"What's happening to him?" her mother murmured, her voice etched with amazement.

Clary shook her head, a single strand of crimson hair falling into her eyes. "I transferred the heavenly fire that was in Jace to the sword. And now it's killing him."

She heard her mother's gasp but ignored it. There was nothing they could do. Stabbing Sebastian had been the plan all along. It was what had to be done. But why did she feel so torn up inside?

As soon as the flames had started, they disappeared, funneling back into the wound in his chest. His ceremonial red robes were blackened and charred.

"Clary," he whispered.

Clary's eyes found his and an iron fist clutched her stomach. His eyes, once jet-black, were changing. An explosion of color lit his irises, spreading until his eyes were a clear, emerald green. And his skin…his skin was darkening slightly, making him look more human. His face was altering as well, the sharp angles softening, the cruel twist of his lips subsiding.

"I don't understand," whispered Clary. She leaned forward and looked closely at the wound in his chest. The torn skin was slowly knitting back together, mending itself.

Sebastian found Clary's limp hand and he clutched it, his grip surprisingly strong for someone that was supposed to be dying.

"Heaven made a mistake," he murmured.

This is it, she thought. He was losing his mind. Why couldn't he just die already and let her be? She didn't know if she could stand much more of this. She closed her eyes, her lashes brushing her cheeks.

Sebastian's hand was warm in hers. How odd. Weren't people supposed to grow cold as the life left them?

Clary heard her mother's sharp intake of breath beside her. Her eyes opened of their own accord.

Sebastian was sitting up, a look of amazement on his face. His eyes were startling green against his gently tanned skin, lined in curling black lashes. His hair had eased from white to the palest blond, and it stuck up from every angle, ruffled and askew.

He reached forward and brushed the strand of hair from Clary's face. His touch was gentle, sending shivers racing across her skin.

"I don't understand," said Clary, her heart beating painfully against her ribs. Her first thought was that this was bad. Very, very bad. The heavenly fire was her only plan, the only way she knew of that could destroy Sebastian. To put an end to this madness. But it hadn't worked.

And yet…

He was different. This was undeniable. It wasn't just his appearance, but his whole aura. Before, hatred and insanity had encased him. Now, he was a different person entirely.

She could hear murmurs from behind her, growing steadily in volume. The Endarkened were getting restless, and she knew it was only moments before they would attack.

Clary watched in amazement as Sebastian stood up, looking regal even in his tattered clothes. He faced the crowd of destroyed Nephilim. Clary turned to see the looks of shock on her friends' faces and the confusion marking the Endarkeneds'.

"Jace, retrieve the Infernal Cup," he said. Even his voice was the different. It had lost all traces of cold indifference.

Jace blinked, stunned, but bent to retrieve the Cup anyway.

"Bring it to me," said Sebastian. His voice wasn't commanding either, simply…pleasant. As if he was asking a simple favor from a dear friend.

Jace's eyes darted to Clary's, and with a thrill of fear she found herself nodding slightly. What was she doing? Sebastian was still alive, she had to kill him! If not, everything would be lost.

But she sat still, besides her mother, paralyzed. Jace walked up the stairs to the dais and handed the Cup to Sebastian, looking perplexed by his own actions.

Sebastian held up the Infernal Cup, the light reflecting off its surface. The room was completely and utterly silent, everyone gazing at Sebastian.

It was then that he threw the Cup, arm bending back gracefully, propelling it forward. It fell in slow motion, the entirety of the room entranced in its motion. It hit the ground and shattered, fracturing into a million pieces.

"Master!" screamed Amatis, stumbling forward. "What have you done?"

There was sorrow in his emerald eyes as he watched her stagger, an emotion that shouldn't have been possible for him.

"I'm sorry," he whispered, his voice filled with soul crushing regret. "I'm so sorry."

The Endarkened fell, one by one. Their pained cries filled the air for a moment, infecting the room with misery. And then they were dead, their corpses littering the room. Silence lingered, each person not brave enough to break it.

Clary stood up, facing her brother. She searched his face, trying to determine what had happened within him.

"Heaven made a mistake," he said again, his voice drifting through the silence. "The heavenly fire should have killed me. There wasn't enough good left in me to allow my survival. But somehow, miraculously, I did. The demon blood in me is gone, burned away."

Clary heard her mother gasp and begin sobbing, burying her face in her lap.

This wasn't possible. There was no way that Sebastian should have survived. And yet he was here, standing before her, looking perfectly healthy yet _changed_.

He stepped away for a moment and Clary stared forward, stunned, everything she thought she knew crumbling around her.

He returned, clutching Heosphoros in his hand. It was still dripping with blackish blood—his blood.

"No!" screamed someone from below the dais.

Isabelle threw herself in front of Clary, pushing her backwards.

"Stay away from her," she snarled, her whip curling down from her wrist, resting in a deadly spiral on the ground.

Sebastian's emerald eyes widened.

"Why would I kill her?" he said, real, actual surprise occupying his tone. "I was simply going to offer her the blade."

Isabelle turned to Clary. This was obviously not the answer she had been expecting. Clary nodded and stepped forward, a mere few feet away from Sebastian.

He held out the blade and she took it, balancing it in her palm.

Her brother spread his arms. "Kill me."

Clary took a step back, revulsion clutching her. "Why?" she wondered, curiosity dominating her voice.

He looked at her, smiling slightly. This smile was so different. It was warm and full of life.

"Heaven made a mistake, and you must right it," he said, as if stating the obvious. "I did terrible things. You know that. Even though that was a different part of me, a part which is no longer there…it was still me, in a way. I don't deserve to live."

Clary paused, levelling the sword at his heart. She didn't know if she could do it again. Especially not with Sebastian like _this_, this different person that she didn't know. This person that should have been alive this whole time, but hadn't gotten a chance, thanks to Valentine.

It was in that moment that she realized she couldn't kill him. She couldn't kill this person—her brother. He wasn't Sebastian at all.

"I'm not going to kill you," she said, her voice shaky. She could feel Isabelle tense up beside her, and her mother's sobs subsided at once. She began again, clearing her throat, her voice strong and steady. "I am not going to kill you, Sebastian."

Sebastian stared at her long and hard.

"Clary, I deserve to die," he whispered, sounding slightly uncertain.

"No," she whispered, tears clouding her vision. "You don't. Sebastian, that monster that landed us in that mess, _he _deserves to die. But you're not him, are you?"

He shook his head slowly, his eyes still fixed on hers.

"No," he said slowly, his voice sad. "I'm Jonathan."

Clary's thoughts were a jumbled mess inside her head, refusing to let her sort them. How was she letting this happen? How could she allow him to live, knowing all the terrible things he had done?

Yet it seemed completely and utterly _wrong _to kill him now, when he was so different. And she knew he spoke the truth. The demon blood had been burned away by the heavenly fire. The demon blood had carried the evil, pumping it through his heart, controlling him. Without it he was a different person entirely.

He was her brother.


	2. Decisions

**I hope you enjoyed the first chapter! This is the first time in about 5 years that I have written fanfiction, so I hope it's not that dreadful. Remember to review with insight on the story and things you liked/didn't like. Please ignore any inaccuracies in the Mortal Instruments world.**

Clary dropped the sword, letting it skitter away from her. Jonathan's eyes followed it for a moment before resting upon his mother.

Jocelyn stood slowly, hastily wiping the tears from her face. Her eyes were puffy and red, but she smiled weakly.

Within the space of time it took to breathe Jocelyn closed the distance between herself and her son, wrapping him in her arms. Jonathan looked surprised at first and his arms draped around his mother awkwardly.

A pang of sadness washed through Clary. Sebastian hadn't been capable of love. He thought that domination was the key. He believed that forcing someone to admire you was love.

But now, Sebastian was gone, replaced by Jonathan. By the look on his face, Clary could tell that he was experiencing love for the first time. Real love, untainted by evil and darkness.

Clary felt a rush of warmth towards her mother. What was she feeling right now, as she embraced the son that had been denied to her all these years? Forced to accept that he was still the same person that had killed so many Shadowhunters and wreaked so much chaos, yet completely and utterly different?

"I hate to defile this beautiful moment, but the portal is closing," said Simon, his voice carrying over the strange scene.

Clary whipped around. The portal was indeed closing, fractures spreading across the image of Idris.

The group turned and raced for the portal. Alec and Magnus disappeared through it first, their hands intertwined. Luke and Isabelle went next, melting into the image. The room began to shake violently.

Clary hung back, watching Jonathan. Jocelyn had broken away from him, and it was obvious she was unsure of what she should do next.

"Go," said Jonathan firmly. "I'll stay. I won't cause you any more trouble."

Clary saw Jace nodding at this, though he looked uncomfortable all the same.

"Come on Clary," said Simon, looking uneasy. "It's what's right."

Clary glanced at her mother's face, seeing the look of incredible sadness. She had just gotten her son back, and she would have to lose him all over again.

"No," said Clary loudly, straining to be heard over the shaking and moaning of the room. "He's coming with us."

Simon and Jace both stared at her, appalled. Jocelyn brought her hand to her mouth, her eyes refilling with tears.

A chunk of the portal broke off and shattered against the floor.

"Now come on, we need to go!" yelled Clary.

She grabbed Simon and Jace both by the arm and hurled herself through the portal, trusting that her mother and Jonathan would follow close behind.

She felt a cool burst of air wash over her, and the world spun dizzyingly.

Clary stumbled to her knees, landing sprawled in a heap against Simon and Jace. Soft grass caressed her legs. She felt bruised all over, mentally and physically.

The air warped ahead of her and Jocelyn emerged, followed by Jonathan. The portal shimmered; revealing one last glimpse of the throne room filled with dead Dark Shadowhunters, before it collapsed in on itself and disappeared.

"Clary, you're crushing my lungs," said Jace softly, breaking the silence.

Clary muttered an apology and sat up. Jace wrapped his arms around her, encircling her in familiar warmth. He curled himself against her, burying his face in her hair.

"Did I do the right thing?" she whispered, just loud enough for him to hear her.

He exhaled, clearly uncertain. "We'll know soon enough," he replied, kissing her cheek gently.

"Would you have killed him?" she asked, letting him hold her. She had never felt more emotionally confused in her life.

"I don't know," he admitted.

There were groans from all around her as the group climbed to their feet. Clary glanced around at her friends and family. Luke wore a look of sadness, mourning the loss of his sister. Magnus and Alec leaned against each other, Magnus whispering something to Alec that made the younger boy's mouth crinkle into a small smile. Isabelle stood facing away from the group, Simon standing at her side awkwardly. Behind them Jonathan stood, looking unsure of himself, while Jocelyn still looked stunned by the return of her son.

Clary realized with a start that it was one thing to pardon Jonathan, but another completely to deal with the consequences. What would they do now? If Jonathan entered Alicante there would be panic. There was no way for Clary to convince everyone that Jonathan was different now. No one would believe her. Where was he supposed to go?

Jocelyn stepped forward. "We have to get Jonathan away from here," she said. "Someone will notice us eventually, and then there will be panic. Most likely we'll be arrested."

"When the gateway to this world was destroyed, it momentarily cut off the defenses of the city," said Jonathan. "For a few minutes we should be able to create a portal out of here."

Everyone looked to Magnus.

"Whoa there," he said, holding up his long-fingered hands. "I know you just had a moment back there, but how do we know that he isn't going to start his madness again once we get out of here?"

"He's not going to," said Clary firmly. How could she explain that she knew? It was more of a feeling deep in her gut, not something based on fact.

"Clary, if we bring him back to New York and he does something, it could be catastrophic," said Luke, his voice sounding hollow.

Jonathan stepped forward.

"I can't say anything to convince you that I changed," he said slowly. "You'll have to take my word for it. I deserve to have stayed in Edom to rot forever, but you chose to bring me here. I offered to let Clary kill me. If there's anything else I can do to prove it to you, I won't hesitate to do it."

There was a moment of tense silence.

"But we don't have much time," he finished. "So if you can make a portal, it's now or never."

Magnus's hands began to twirl and dance through the air, golden sparks lacing the air with energy. A doorway formed in front of him, gradually gaining depth.

It finished forming. It hung in the air, a gateway to swirling oblivion.

"Right this way," said Magnus stiffly. It was evident that he didn't believe Jonathan had really changed.

Simon and Isabelle disappeared through the portal, followed by Luke and Jocelyn. Alec said something to Magnus, who nodded, before he too disappeared. Jonathan went next, stepping through the gateway almost tentatively, as if unsure of what he would find on the other side.

Clary stepped up to the portal.

"Let us hope that you have made the right choice," said Magnus. There was no trace of humor in his voice, only seriousness. A chill rushed down her spine.

As she stepped through the portal, Jace close behind, she hoped with all her heart that she had made the right choice.

Otherwise, the consequences would be deadly.


	3. Comfort

The group emerged in front of the Institute. The familiar bustling noises of New York surrounded them. The sky was dark, stars sparkling brilliantly up above, accompanied by a beaming full moon.

The group stood facing each other, no one quite sure of what to say. They were all exhausted and in need of a bath. It was obvious what they were all thinking, though no one spoke.

Clary's eyes darted to Jonathan, who was standing a bit apart from everyone else, looking down at his feet.

"Well, we will be going then, while you sort this unpleasantness out," said Magnus airily, breaking the silence.

"We?" asked Alec, his voice hopeful.

"What, you thought we were going to hook up in the demon dimension and then never speak again?" asked Magnus, his cat eyes narrowing.

Alec shook his head, smiling slightly. "Alright, alright."

He patted Jace on the shoulder and followed the warlock into the night.

"I should be going as well," said Isabelle. "Do you want to come?" she added, to Simon.

He glanced up at the Institute looming over them. "I would, but being damned and all…I feel like it would be a shame to die tonight, after everything we've been through."

"We could go to your apartment," she said softly. For the first time Clary saw something like uncertainty in her eyes. Isabelle was always so confident, never needing to ask what to do. Had something finally happened between them?

Simon nodded. "You okay Clary?" he shot a suspicious look at Jonathan.

Clary smiled at him, though it must have looked forced. "I'm fine," she said quietly. Simon stepped forward and gave her a hug. Clary hugged him back, relishing the familiarity. She was beginning to realize that she had changed things irrevocably by bringing Jonathan here.

They walked away, the darkness swallowing them up.

All that was left was Clary, her mother, Luke, and Jonathan and Jace. At the moment Clary wanted nothing more than to go home and sleep, leaving the consequences of her decisions behind her. She couldn't help but feel like a storm was coming, a storm that she undoubtedly had caused.

"I'm going to my apartment," said Luke suddenly. "Would you like me to take Clary?" he added. It was obvious that he didn't trust Jonathan, and he had good reason not to. He was the reason Amatis was dead, the reason that hundreds of Shadowhunters were dead.

"I'll take Jonathan to the Institute," said Jace. "I'll make sure he doesn't get up to no good."

Jace smiled weakly. He too looked drained and exhausted, covered in grime and dirt. Clary was sure she looked the same.

"Are you sure you'll be okay?" asked Clary nervously. She didn't like the idea of leaving Jace alone with Jonathan, especially with what had happened last time.

"I think you're forgetting who you're speaking too," said Jace. "While I may be blindingly good looking, I am also a trained demon hunter. I think I can handle another teenage boy."

_Except he's not your average teenage boy_, thought Clary. She shook her head. They couldn't stand out here forever, and this was the best option. She needed time away from Jonathan to sort out her thoughts. Plus, she would get to go home. The thought filled her with warmth.

"I won't cause any trouble," promised Jonathan. His eyes were shadowed due to the darkness, and for a shivering moment Clary imagined she could see Sebastian reemerging. She turned away quickly.

"I'll see you tomorrow, Jace," she said.

He smiled, flashing his pearly teeth. "Good night."

Alec entered the apartment, still amazed that this was really happening. For a moment his worries about Jonathan were melting away, replaced by pure happiness. Magnus still loved him.

The apartment was brightly colored, with canary yellow walls and white furnishings. Alec wondered if Magnus's living space reflected his emotions, and if so, the bright colors were a good sign.

Alec took a deep breath, smelling the familiar scents he associated with Magnus—the sweet zing of his hairspray, the rich odor of coffee, and the sensual hints of his favorite cologne.

"I'm going to go change," said Magnus, sounding exhausted but pleased all the same. "Do you want anything?"

"Sure," said Alec. He was still wearing his filthy Shadowhunter garb. "But nothing with glitter, sparkles, mesh or rainbow pattern," he added quickly.

Magnus groaned from the other room. "Alexander, you do realize you just eliminated over half my wardrobe?"

Alec shook his head and plopped himself down on the white couch. He had missed his eccentric boyfriend more than he wanted to admit. The war had been hard on him, but now it was over—he hoped. It was unsafe to say that the conflict would cease completely, due to the fact that Sebastian—Jonathan, he corrected himself—was still alive.

He was furious that Clary had let him live. If it was up to him, he would have killed Sebastian on the spot. After all, Sebastian was the one that had murdered Max. That was something that he would never, ever forget and never forgive him for. He had a feeling deep in his gut that there was something seriously wrong with Jonathan, even though the demon blood had been burned from his system.

Magnus emerged from the bedroom, dressed in pajamas—a loose violet t-shirt and black sweatpants patterned with cupcakes. He was holding a bundle of clothing, which he tossed to Alec.

Alec unfolded the bundle, finding a plain gray sweater and black pj bottoms. He was surprised that Magnus even owned something so drab.

"Thanks," said Alec, grateful for the clothes. He headed off to the bathroom to change and wash up.

After a hot shower he emerged smelling strongly of sandalwood (Magnus's preferred scent). He toweled his black hair dry, reducing it to a straggly mess that fell into his eyes. Once he had changed he felt much better. Now all he had to do was scrub the memories off himself, a task that would be significantly harder.

Magnus was waiting in the living room, his long legs draped over the side of the couch. He was rubbing his eyes, removing excess glitter that Alec would undoubtedly find days later in strange places.

Alec sat down beside his boyfriend, their shoulders touching.

"I'm worried," said Magnus, breaking the silence.

Alec's heart sped up. After all that, was Magnus going to break up with him anyway?

"Why?" asked Alec nervously, tugging at the hem of his sweater absentmindedly.

"Sebastian. Jonathan. Whatever the hell you want to call him."

Alec's shoulders slumped with relief. So this wasn't about their relationship after all.

"I don't trust him," said Alec. "It's just like Clary to do something like this, to jeopardize everything we've worked for with one quick decision. He deserves to be dead or at least trapped in the demon dimension where he'll never escape," he finished bitterly.

Magnus turned and looked at him, his gold-green eyes softening thoughtfully. "This is about Max, isn't it?"

Alec looked down at his hands. "No. Yes. I don't know. I know I shouldn't base my judgment completely off of my personal feelings, but there's something wrong with Jonathan. He may be different now, but I think she's forgetting all of the things he's done."

"Agreed," said Magnus softly, finding Alec's hand and lacing his long fingers through his. "And the implications will be awful. Jia Penhallow will have discovered by now that we've escaped and have disappeared…"

Alec sighed and leaned his head against Magnus's shoulder, their hair mingling.

"I swear, if he turns evil overnight and does something, I'll kill him myself," said Alec seriously. He, unlike Clary, had no complicated personal feelings toward Jonathan.

"I love it when you're all vengeful like this," said Magnus, laughing gently. He put a finger underneath Alec's chin and tilted his face up towards his.

"I missed you so much," whispered Alec. He winced inwardly. He hoped that he didn't sound too needy.

"The feeling is mutual, Alexander," replied Magnus.

The space between them vanished in an instant. Their lips collided, desperate to make up for their time apart.

Alec sighed with contentment as Magnus stroked his tangled hair, pushing it away from his face. Alec wrapped his arms around the warlock, holding him close.

Warmth was spreading through Alec, warmth dismissing the blanket of cold that had possessed him ever since they had split up. At last he felt whole again, safe in Magnus's arms. Whatever happened next, he would be fine. His sparkly guardian angel was beside him once more.

**I hope you enjoyed this chapter! I figured that since this story is happening right after CoHF, there should be some explanation of what happens between Alec and Magnus. Plus they're just adorable together, so I couldn't resist. Remember to leave comments! I love feedback and it will help me improve the story. I will be updating soon!**

**~SQuid**


	4. Exhaustion

Jace led Jonathan into the Institute, their feet echoing softly through the huge empty space. Jonathan was silent as they walked through the empty hallways.

They made it to the corridor lined with bedrooms. Jace figured he would be able to keep a close watch on him if he picked a room close to his personal sleeping quarters.

"Jace," said Jonathan softly. "You know more than anyone that I shouldn't be here."

Jace nodded. He _did _know. But at the same time, in a small corner of his heart, he was glad that Clary had spared him. Jonathan knew him in a way that no one, not even Alec, his _parabatai_ did. The time they had spent bonded together had brought them close, and the bond they shared continued even after they were severed apart. Though Jace would never admit it to anyone, a small part of him had enjoyed the time they had spent together in apartment.

"I know," Jace said. "I'm still convinced that any moment now you're going to pull me aside and start plotting some sort of sick scheme."

Jonathan winced, something that would have been completely out of character for Sebastian.

Jace wasn't sure that he liked this version of Jonathan. As he had gotten to know Sebastian, he had learned that he complemented his severity. Jace had been the flames to melt Sebastian's ice—even if only a little. Sure, Sebastian had been completely insane, driven only by his own motives, void of any feeling. But there was something about that cruel motivation that Jace had admired.

"I should be dead," said Jonathan seriously. "Dead, or trapped in that demon dimension—"

"Well you're not, okay?" snapped Jace. Jonathan took a step back, surprised by Jace's tone. "Clary chose to not kill you, and I'm going to honor that decision. Yes, you deserve to be dead; it's simply a mistake that kept you alive. But you're here now, and that's all that matters."

Jonathan's mouth curved into a small smile. Jace marveled at how different it was than before. Sebastian's smiles had always held a sort of deadly elegance—they were charming, if you couldn't see past the curtain into his eyes. A viper right before it killed you. But Jonathan's smile, it was real.

Jace realized that while this boy standing in front of him still looked like Sebastian, still had his voice, still possessed all of the memories before he changed, he was a completely different person.

Was there a possibility that Jonathan's evil ways were gone? It seemed unlikely, but every instinct told Jace that this was true. But how could he know for sure?

"Go to bed, Jonathan," said Jace tiredly. "I'll see you tomorrow."

Jonathan nodded and started to walk towards one of the empty bedrooms.

"Jace?" he said suddenly, sounding a bit nervous.

Jace stopped walking and turned slowly. "What is it now?" he asked impatiently.

"Will I be able to talk to Clary tomorrow?"

Jace closed his eyes.

"I don't know," said Jace. He didn't want Jonathan with Clary ever again, not with what he had almost done. But then again, the only reason he was standing here in front of him was because of Clary.

Jonathan blinked, probably sensing what Jace was thinking. Without another word he turned and disappeared into the bedroom, closing the door with a click.

Jace sighed. This was going to be a lot more complicated than he thought.

**What do **_**you**_** think will happen when Jonathan gets to talk to Clary after all this? Review! Updates on the way!**

**~SQuid**


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